# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
#
# Copyright 2021 The NiPreps Developers <nipreps@gmail.com>
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
# We support and encourage derived works from this project, please read
# about our expectations at
#
# https://www.nipreps.org/community/licensing/
#
"""Wrappers of NiTransforms."""
from pathlib import Path
from nipype.interfaces.base import (
TraitedSpec,
BaseInterfaceInputSpec,
File,
SimpleInterface,
InputMultiObject,
traits,
isdefined,
)
XFM_FMT = {
".lta": "fs",
".txt": "itk",
".mat": "itk",
".tfm": "itk",
}
class _ConcatenateXFMsInputSpec(BaseInterfaceInputSpec):
in_xfms = InputMultiObject(File(exists=True), desc="input transform piles")
inverse = traits.Bool(False, usedefault=True, desc="generate inverse")
out_fmt = traits.Enum("itk", "fs", usedefault=True, desc="output format")
reference = File(
exists=True,
desc="reference file (only for writing LTA format, if not "
"concatenating another LTA).",
)
moving = File(
exists=True,
desc="moving file (only for writing LTA format, if not "
"concatenating another LTA).",
)
class _ConcatenateXFMsOutputSpec(TraitedSpec):
out_xfm = File(exists=True, desc="output, combined transform")
out_inv = File(desc="output, combined transform")
[docs]
class ConcatenateXFMs(SimpleInterface):
"""Write a single, flattened transform file."""
input_spec = _ConcatenateXFMsInputSpec
output_spec = _ConcatenateXFMsOutputSpec
def _run_interface(self, runtime):
out_ext = "lta" if self.inputs.out_fmt == "fs" else "tfm"
reference = self.inputs.reference if isdefined(self.inputs.reference) else None
moving = self.inputs.moving if isdefined(self.inputs.moving) else None
out_file = Path(runtime.cwd) / f"out_fwd.{out_ext}"
self._results["out_xfm"] = str(out_file)
out_inv = None
if self.inputs.inverse:
out_inv = Path(runtime.cwd) / f"out_inv.{out_ext}"
self._results["out_inv"] = str(out_inv)
concatenate_xfms(
self.inputs.in_xfms,
out_file,
out_inv,
reference=reference,
moving=moving,
fmt=self.inputs.out_fmt,
)
return runtime
[docs]
def concatenate_xfms(
in_files, out_file, out_inv=None, reference=None, moving=None, fmt="itk"
):
"""Concatenate linear transforms."""
from nitransforms.manip import TransformChain
from nitransforms.linear import load as load_affine
xfm = TransformChain(
[load_affine(f, fmt=XFM_FMT[Path(f).suffix]) for f in in_files]
).asaffine()
if reference is not None and not xfm.reference:
xfm.reference = reference
xfm.to_filename(out_file, moving=moving, fmt=fmt)
if out_inv is not None:
inv_xfm = ~xfm
if moving is not None:
inv_xfm.reference = moving
inv_xfm.to_filename(out_inv, moving=reference, fmt=fmt)